ClinVar Genomic variation as it relates to human health

This variant has been previously reported as a compound heterozygous and a heterozygous change in patients with methylcobalamin deficiency G (cblG) disorder (PMID: 8968736, 12068375). Functional studies of methionine synthase activity a fibroblast cell line from a patient carrying this variant showed a 30-fold reduction in enzymatic activity relative to controls, in the presence of NADPH (PMID: 9235907). It is present in the heterozygous state in the gnomAD population database at a frequency of .006% (14/243760) and thus is presumed to be rare. The c.3518C>T (p.Pro1173Leu) variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. Based on the available evidence, the c.3518C>T (p.Pro1173Leu) variant is classified as pathogenic.

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 24664876, 9235907, 33726816, 28666289, 32581362, 8968736, 12068375, 34625984)

Variant summary: MTR c.3518C>T (p.Pro1173Leu) results in a non-conservative amino acid change located in the Vitamin B12-dependent methionine synthase, activation domain (IPR004223) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 6.4e-05 in 218506 control chromosomes. c.3518C>T has been reported in the literature in multiple individuals affected with Methylcobalamin deficiency type cblG (e.g. DeBiase_2020, Watkins_2002). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 32533987, 12068375). Eight submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 1173 of the MTR protein (p.Pro1173Leu). This variant is present in population databases (rs121913578, gnomAD 0.01%). This missense change has been observed in individual(s) with methionine synthase deficiency (cblG) (PMID: 9235907, 12068375, 25526710). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 14278). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt MTR protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.

MTR: PM3:Strong, PM2, PP4:Moderate, PP3, PS3:Supporting

The MTR c.3518C>T (p.Pro1173Leu) is a missense variant that has been reported in at least six studies, in which it was identified in a compound heterozygous state in 14 individuals and in a homozygous state in two individuals, all diagnosed with disorders of intracellular cobalamin metabolism (Gulati et al. 1996; Gulati et al. 1997; Watkins et al. 2002; Wong et al. 2015; Alazami et al. 2015; Komulainen-Ebrahim et al. 2017). Watkins et al. (2002) performed haplotype analysis and determined that the c.3518C>T transition in a CpG island has occurred independently on at least two separate genetic backgrounds. Fibroblast cells from a female, homozygous for the p.Pro1173Leu variant and diagnosed with severe macrocytic anemia at three months, showed 9 % methionine synthase activity compared to the reference, the level of MTR protein was also reduced in these cells compared to control. The p.Pro1173Leu variant was absent from 210 control subjects and is reported at a frequency of 0.000349 in the American European population of the Exome Sequencing Project. Based on the collective evidence, the p.Pro1173Leu variant is classified as pathogenic for disorders of intracellular cobalamin metabolism. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

The p.P1173L alteration is located in exon 33 of the MTR gene (NM_000254). This alteration results from a C to T substitution at nucleotide position 3518, resulting in an amino acid substitution of leucine for proline at position 1173, an amino acid with dissimilar properties. This alteration (HGMD # CM961003) was first reported in a compound heterozygous state with a 3bp in-frame deletion in a cbIG deficiency patient (Gulati et al. (1996) Hum Mol Genet 5, 1859). It is likely a founder mutation among individuals of European ancestry, consistent with the family's reported ancestry (Rutsch F, et al. (2011) J Inherit Metab Dis 34:121-126, Watkins D, et al. (2002) Am J Hum Genet 71:143-153). The c.3518C>T (p.P1173L) alteration in the MTR gene is the most common alteration, observed at a frequency of about 40% (16/38 chromosomes), in patients with cblG deficiency (Watkins D, et al. (2002) Am J Hum Genet 71:143-153). This variant was previously reported in the SNPDatabase as rs121913578. Based on data from the NHLBI Exome Sequencing Project (ESP), the T-allele has an overall frequency of approximately 0.03% (4/12,990) total alleles studied. The T-allele was observed in 0.03% (3/8,588) European American alleles and in 0.02% (1/4,402) African American alleles studied. To our knowledge, this alteration has not been previously reported in the 1000 Genome database. This amino acid is completely conserved in available vertebrate species. This variant is predicted to be probably damaging by Polyphen and deleterious by SIFT in silico analyses respectively. Based on the available evidence to date, this variant is classified as a pathogenic mutation.